How to import obj and convert and export as fbx from command line in Python
The link @HikariTw should give you an answer; for example on my system the path to Blender is /Applications/Blender.app/Contents/MacOS/Blender.  The error you're getting is because the Blender binary isn't in your path.
As for importing/exporting; your script should be pretty simple, just remove the default cube, call bpy.ops.import_mesh.stl to import and bpy.ops.export_scene.fbx to export.